tidk v0.2.62 #50836
tidk v0.2.62 #50836
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces updates to the Changes
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/tidk/build.sh (1)
4-4: LGTM! Consider removing the --verbose flag for production builds.The changes look good. The addition of
OPENSSL_DIR=$PREFIXensures that the correct OpenSSL library is used during the build process, which is important for consistency and reproducibility.Consider removing the
--verboseflag for production builds to reduce log output. You can keep it commented out for debugging purposes:-C_INCLUDE_PATH=$PREFIX/include OPENSSL_DIR=$PREFIX LIBRARY_PATH=$PREFIX/lib cargo install --verbose --path . --root "${PREFIX}" +C_INCLUDE_PATH=$PREFIX/include OPENSSL_DIR=$PREFIX LIBRARY_PATH=$PREFIX/lib cargo install --path . --root "${PREFIX}" +# Use the following line for verbose output during debugging: +# C_INCLUDE_PATH=$PREFIX/include OPENSSL_DIR=$PREFIX LIBRARY_PATH=$PREFIX/lib cargo install --verbose --path . --root "${PREFIX}"recipes/tidk/meta.yaml (1)
30-30: Consider expanding test commandsThe test command has been simplified to
tidk -h, which might not provide comprehensive coverage of the package's functionality.Consider expanding the test commands to ensure thorough testing of the package. A more comprehensive approach could be:
test: commands: - tidk -h - tidk --version - tidk --helpThis would verify both the basic functionality and the version information, providing better assurance of the package's correct installation and operation.
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📒 Files selected for processing (2)
- recipes/tidk/build.sh (1 hunks)
- recipes/tidk/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/tidk/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/tidk/meta.yaml (4)
1-1: LGTM: Version updateThe version has been correctly updated to "0.2.62" as per the PR objectives.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-20: LGTM: Added Rust compiler to build requirementsThe addition of the Rust compiler to the build requirements is likely necessary for the new version of the package.
Please ensure that adding the Rust compiler doesn't conflict with existing build requirements or cause any issues in the build process. You may want to test the build locally to confirm compatibility.
25-27: LGTM: Added OpenSSL to host requirementsThe addition of OpenSSL to the host requirements is likely necessary for the new version of the package.
Please confirm that the addition of OpenSSL is indeed necessary for the new version and doesn't conflict with existing requirements. You may want to check the package's documentation or release notes to verify this dependency.
13-14: LGTM: Source URL and SHA256 updateThe source URL has been updated to include the "v" prefix, which is a common practice. The SHA256 checksum has also been updated for the new version.
Please verify the correctness of the SHA256 checksum. You can use the following command to double-check:
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@Euphrasiologist the build seems to be failing because when the test command runs, So |
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Thank you @mbhall88 - that was a really silly bug... I've fixed it now thank you so much! |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/tidk/meta.yaml (1)
30-30: Consider retaining both test commands for better coverage.The test command has been simplified to
tidk -h. While this checks the basic functionality, it might not be sufficient to ensure the package is working correctly. The previous version tested both the help output and the version information, which provided more comprehensive verification.Consider updating the test commands to:
test: commands: - tidk -h - tidk --versionThis will ensure that both the help output and version information are correctly displayed, providing better test coverage.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- recipes/tidk/meta.yaml (2 hunks)
🧰 Additional context used
🪛 yamllint
recipes/tidk/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/tidk/meta.yaml (4)
1-1: Version update looks good.The package version has been updated from 0.2.41 to 0.2.63, which aligns with the PR objective to update the tidk package.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
20-20: Build requirement addition looks appropriate.The Rust compiler has been added to the build requirements, which suggests that the package now requires Rust for building. This change is likely related to updates in the package's build process or dependencies.
To confirm the necessity of Rust in the build process, let's check the package's build instructions:
Please review the output to ensure that Rust is indeed required for building the package.
✅ Verification successful
Let's correct the shell script to accurately verify the presence of Rust-related build instructions:
Rust dependency confirmed as required for build.
The Rust compiler has been added to the build requirements, and the package's README.md confirms the necessity of Rust and cargo for building the package.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for Rust-related build instructions in the package repository curl -sL https://raw.githubusercontent.com/tolkit/telomeric-identifier/v0.2.63/README.md | grep -i 'rust\|cargo'Length of output: 203
Script:
#!/bin/bash # Corrected shell script to check for Rust-related build instructions in the package repository curl -sL https://raw.githubusercontent.com/tolkit/telomeric-identifier/v0.2.63/README.md | grep -i 'rust\|cargo'Length of output: 737
13-14: Source URL and checksum updates look correct.The source URL format has been updated to include a "v" prefix, which likely reflects the new versioning scheme in the source repository. The SHA256 checksum has also been updated to match the new version.
To ensure the integrity of the package, let's verify the checksum:
Please compare the output of this command with the checksum in the meta.yaml file.
25-27: Host requirement addition looks appropriate.OpenSSL has been added to the host requirements, which suggests that the package now depends on OpenSSL. This change might be related to new features or dependencies in the updated version.
To confirm the necessity of OpenSSL, let's check the package's dependencies:
Please review the output to ensure that OpenSSL is indeed required by the package.
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@BiocondaBot please add label |
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Ps you can remove the OpenSSL dependency by switching to the rustls-tls feature in reqwests e.g. I did this recently and made it a lot easier to build for multiple targets https://github.com/mbhall88/nohuman/blob/6578dfc5743e5d85902ff83f554dd446cc9670c6/Cargo.toml#L25 |
Update tidk to v 0.2.62.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
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@BiocondaBot please update@BiocondaBot please add labelplease review & mergelabel.@BiocondaBot please fetch artifactsYou can use this to test packages locally.
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@bioconda/<team>and will automatically re-post them to notify the addressed<team>.Summary by CodeRabbit
New Features
tidkpackage to version 0.2.63 with improved installation commands.Bug Fixes
--verboseflag for better diagnostics.Documentation